Microbiology Commons^™

Investigation Of Biological Denitrification Inhibition By Specific Anthocyanins, Kristin Palazzo, Holly Anderson, Aislinn Geedey, Angela Kent

MICRO-CCS student projects

Nitrogen fertilizers are applied to corn fields to support high crop yields, but some nitrogen is lost through microbial denitrification, producing nitrous oxide (N2O), a potent greenhouse gas. Some plants produce certain flavonoids that can suppress microbial denitrification, a trait known as biological denitrification inhibition (BDI). Maize produces flavonoids in the form of anthocyanins, including cyanidin-3-glucoside (C3G), the major anthocyanin produced by maize.

The goals of this project were to determine whether C3G:

is produced in maize roots

inhibits microbial denitrification

Recovering Plasmid-Id Barcoded Strains Of Sinorhizobium Meliloti From A Native Soil Microbiome, Kenny Sacks, Hannah Murray, Katy Heath

MICRO-CCS student projects

Introduction

Legume-Rhizobia Mutualism: Nitrogen is an essential nutrient for plant growth. Plants can’t produce nitrogenous compounds. Rhizobia fix atmospheric nitrogen gas into bioavailable forms. Rhizobia form a nutrient exchange mutualism with leguminous plants.

Project description

Can our bacteria persist within the rhizosphere and into the nodule when faced with native microbial competitors? The Medicago-Sinorhizobium mutualism is used as a model system. Survival of strains post competition is difficult to measure due to identical 16S rRNA sequences and similar marker genes. Plasmid-ID barcoding sequences may provide a way of testing strains against a community.

Soil Microbiome Effect On Seedling Diseases And High Throughput Isolate Identification, Annalaysia Smith, Mara Krone, Santiago Mideros

MICRO-CCS student projects

The soil microbiome has a substantial effect on disease suppression. Organic farming is a practice used to create a more diverse microbiome which can create disease suppression. Different agricultural practices such as fertilization and rotation system are known to affect the microbiome (Schlatter et al 2017). Therefore, it is important to study the effects of different microbiomes on disease suppression. Furthermore, methods are necessary for quantifying the effect of disease suppression on specific pathogen populations. To do this, it is important to properly identify the pathogens.

Objectives:

1. Test if different nitrogen treatments cause variations in organic soils disease suppression. …

Effects Of Varying Ph Levels On Prophenoloxidase Activity And Hemocyte Recruitment In Daphnia Dentifera, Yusra Siddiqi, Carla Caceres

MICRO-CCS student projects

Anthropogenic activities and natural processes are responsible for changing the pH of freshwaters which can impact aquatic life. D. dentifera is a keystone species found in midwestern lakes that is susceptible to a parasitic yeast called Australozyma monospora. A. monospora spores puncture the Daphnia gut into the hemolymph and begin using the host’s resources. Invertebrate immunity is under researched.

Research objective: How will different pH impact prophenoloxidase (proPO) activity and hemocyte recruitment in Daphnia dentifera?

Screening A Random Hile Mutant Library To Characterize Hild Regulation In Salmonella, Danista Kannah, Gracious Donkor, James M. Slauch

MICRO-CCS student projects

Salmonella is a leading cause of gastrointestinal diseases globally. It utilizes a type three secretion system (T3SS) encoded on Salmonella Pathogenicity Island 1 (SPI1) to invade host intestinal epithelial cells during infection.

HilE directly regulates HilD via a direct protein-protein interaction. The Slauch lab identified two HilD variants, A141V and A141T, which are blind to HilE. These variants activate hilA expression even in the presence of HilE, indicating that the binding of HilE to these mutants is compromised.

Hypothesis: Performing random mutagenesis of hilE could lead to changes at the protein level which could compensate for the loss of interaction …

Fungal Diversity In Lespedeza Cuneata Roots, Gwendolyn Happ, Sophia Mcdade, Anthony Yannarell

MICRO-CCS student projects

Background

• Plants form a relationship with fungi that can be beneficial or harmful
• Fungi may grow on the plant surface, within plant tissues, or around roots
• Plants release compounds that invite fungi to their roots and chemicals  that can diminish unwanted fungi

Why Lespedeza cuneata? 

• Invasive that competes with native plants and damages biodiversity within plant and animal communities
• Alters soil microbiome
• Expansive seed bank and deep root system
• Understanding its microbiome can help in understanding invasive species success and ecology

Efficacy And Evolutionary Dynamics Of 222 Nm Far-Uvc Against Vibrio Cholerae, Kadicha Madakimova, Angus Wu, Nkrumah Grant

MICRO-CCS student projects

The Far-UVC light at 222 nm wavelength (UV222) is one of the emerging methods of disinfection of bacteria in public spaces such as hospitals and labs.

• Does not penetrate human skin and does not cause harm to eyes making it a safer alternative to conventional UV systems.

• Primarily targets proteins preventing regrowth and repair pathways.

However, the potential for bacterial adaptation following sublethal UV222 exposure remains largely unknown.

Central question: How does QS transcriptional state influence the efficacy and resistance profile of V. cholerae to UV222 nm irradiation?

Hypothesis: Qurom-sensing transcriptional state determines V. cholerae susceptibility to UV222 nm UV …

A Tale Of Two Symbionts: Comparative Cellular Localization Of Two Manipulative Rickettsiella Strains In A Spider, Kaitlyn Costanza, Thea Bliss, Matthew Doremus

MICRO-CCS student projects

Many arthropods harbor maternally transmitted endosymbionts that manipulate host reproduction to increase their transmission. One such manipulation is cytoplasmic incompatibility (CI), in which embryos produced by infected males and uninfected females fail to develop.

Rickettsiella has recently been discovered to cause CI in Mermessus fradeorum. Two geographically distinct Rickettsiella strains infect this spider: R1 causes strong CI, whereas R2 causes weaker CI.

Hypothesis: H1: Both Rickettsiella strains will localize within or near developing sperm cells in the testes. H2: The stronger R1 strain will exhibit more consistent localization within infected adult reproductive tissues than the weaker R2 strain.

Identification Of Conditionally Essential Genes Required For Salmonella Enterica Serovar Typhimurium Adaptation To The Chicken Cecal Extract Through Ex Vivo Modeling And Transposon Insertion Sequencing, Deborah Bukola Olubanjo

Graduate Theses and Dissertations

Salmonella enterica serovar Typhimurium (S. Typhimurium) remains a major foodborne pathogen associated with chicken, where it can persist in the intestinal tract without overt disease and contribute to zoonotic transmission. The chicken cecum represents a complex ecological niche shaped by microbial competition, host-derived substrates, short-chain fatty acids, oxygen limitation, extracellular components, and diverse metabolic gradients. Although transposon insertion sequencing (Tn-seq) has been widely used to define bacterial fitness determinants, limited work has examined genome-wide adaptation of S. Typhimurium in chicken ceca-derived ex vivo systems that preserve key features of the avian cecal environment. This dissertation investigated conditionally essential genes required …

The Deep Darkness Microbiome: Functional And Taxonomic Diversity In An Oligotrophic Temperate Cave, Philips O. Akinwole, Nina G. Shaffer '25, Emma E.C. Jacobs '25, Zoe Green '27, Thi Doan '27, Crimson Hickman '28, Kaija M. Carr '25, Kenneth L. Brown

Biology Faculty publications

Many subterranean ecosystems are chronically energy limited, yet the mechanisms governing microbial community assembly and metabolic function under extreme carbon scarcity remain poorly resolved. We combined 16S rRNA gene sequencing with community-level physiological profiling (CLPP) to examine how physicochemical gradients regulate microbial diversity and carbon-use strategies across a surface-subsurface transition into the Deep Darkness zone of Indiana Caverns. Progressive isolation from surface inputs resulted in sharp declines in microbial biomass, total organic carbon, and nitrogen, accompanied by increased water content and C:N ratios, indicating strong attenuation of allochthonous organic matter and intensified resource filtering. Microbial communities spanned 42 bacterial phyla, …

Endophytic Actinobacteria: Deciphering Therapeutic And Industrial Potential, And Prospects Of Genome Mining In Novel Products Discovery, Yusra Waheed, Rabia Shahdin, Imran Sajid

Journal of Bioresource Management

Endophytic actinobacteria are a diverse group of Gram-positive bacteria with high G+C content, which inhabit plants’ internal tissues, and represent a significant yet underexplored reservoir of bioactive secondary metabolites. In host plants, a remarkable repertoire of metabolites, including broad-spectrum antibiotics, anticancer, antiviral, antifungal, antioxidant, and immunomodulatory compounds, is synthesized by these microbial allies, carrying significant medicinal and agricultural potential. These endophytes, in contrast to their soil relatives, have developed unique biosynthetic gene clusters (BGCs) strongly influenced by plant-associated factors, leading to the production of structurally novel metabolites. In recent years, the advances in genome mining, metagenomics, and metabolomics have accelerated …

Mobile Genetic Elements Shape Microbial Diversity And Functions In Thawing Permafrost Soils, Jiarong Guo, Samuel T. N. Aroney, Guillermo Domínguez-Huerta, Derek Smith, Dean Vik, Carlos Owusu-Ansah, Akbar Adjie Pratama, Sergei Solonenko, Funing Tian, Cristina Howard-Varona, Zhi-Ping Zhong, Aminata Fofana, Garrett J. Smith, Suzanne B. Hodgkins, Dylan Cronin, Isogenie Field Teams 2010–2017, 2019, Emerge Coordinators, Ben J. Woodcroft, Gene W. Tyson, Virginia I. Rich, Matthew B. Sullivan, Simon Roux, Sarah C. Bagby, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current …

Biofilm Formation By Histophilus Somni On 3d Bovine Respiratory Tissue Cultures, Bindu Subhadra, Neeti Gandhi, Dianjun Cao, Yue-Jia Lee, Padmavathy Rajagopalan, Thomas J. Inzana

Faculty Publications - Biological Sciences

The development of bacterial biofilms following infection involves bacterial attachment to tissues and maturation of the biofilm matrix (BM). However, studying the development of bacterial biofilms in vivo is difficult to follow. An established example of biofilm formation during host infection is bovine respiratory disease (BRD) due to Histophilus somni. To more accurately investigate in vivo biofilm development, three-dimensional bovine airway organoids comprised of bovine turbinate epithelial (BE) and pulmonary artery endothelial (BAE) cells embedded in type I collagen were developed. Cell-free concentrated culture supernatant (CCS) from biofilm-grown H. somni suppressed proliferation of epithelial cells more than endothelial cells, affected …

Closing The Gaps: Reforming Maryland Controls On Veterinary Antimicrobial Distribution, Samantha Capaldo, Kerry Mcclaughry

Journal of Food Law & Policy

Antimicrobials have been used in livestock and other food animals in the United States (“U.S.”) since the late 1940s. An antimicrobial is “[a]ny natural, synthetic, or semisynthetic substance that can eradicate or prevent the growth of microbes,” including “[a]ntibacterial, antifungal, antiparasitic, and antiviral medications.” Antimicrobial use in food animals is subject to a complex statutory and regulatory framework at both the state and federal levels. Antimicrobial use in food animals has been widely criticized for contributing to antimicrobial-resistant bacterial infections in humans. In response to this criticism, the U.S. Food and Drug Administration (“FDA”) and several states, including Maryland, have …

Promiscuous Mutualisms: John Dupré And The Centrality Of Symbiosis In The Living World, Thomas Pradeu

Presidential Fellows Articles and Research

My goal in this chapter is to show that symbiosis, especially symbiotic interactions between ‘macrobes’ (non-microbial organisms) and microbes, is a central topic in John Dupré’s work. This topic is undeniably one of the topics by which Dupré has gained wide recognition among practicing scientists, in addition to his recognition within the philosophical community. I spell out why symbiosis has turned out to be a sort of ideal trope for Dupré, as it encapsulates many of his main personal themes—from promiscuous realism to process ontology. I then show that immunology offers one interesting and complementary entry point into microbial symbiosis …

Describing Propagation Of Carbapenem-Resistant Acinetobacter Baumannii Through Comparative Genomics And Phenotypic Analysis Of Modern-Day Clinical Isolates, Emma Graffice

ETDs from 2020-2029

Understanding the genomic structure of bacterial populations is essential for tracking antimicrobial resistance and informing public health strategies to prevent spread of multidrug resistant organisms. In this study, we investigated the diversity and distribution of carbapenem-resistant Acinetobacter baumannii (CRAb) lineages across a major healthcare system in the U.S. Deep South through both retrospective and prospective isolate collection. Our analysis revealed a heterogeneous population composed of multiple genotypically and phenotypically distinct lineages. To improve the resolution of lineage classification, we applied average nucleotide identity (ANI) as a high-resolution metric for comparative genomics. A ≥99% ANI threshold effectively delineated lineages, outperforming traditional …

Jnk Signaling Impacts Car-T Cell Effector Function, Charles Kuhlmann

ETDs from 2020-2029

The potent cytotoxic activity of T cells serves as a natural defense against cancers. Chimeric antigen receptor (CAR) T cell therapy represents a strategy for harnessing T cells against advanced tumors. CAR-T cell therapy has seen striking success against hematologic malignancies, prompting its application to new diseases. Ovarian cancer is a highly lethal disease characterized by frequent recurrence and aggressive nature, prompting the investigation of CAR-T cell therapy as a salvage regimen. However, like in other solid tumors, the early performance of CAR-T cell therapy in ovarian cancer is poor. While many strategies exist for improving the longevity of CAR-T …

Dual-Action Antibacterial Agents Targeting Biofilm Reduction And Membrane Disruption In Staphylococcus Aureus, Rahmat Folashade Zakariyah, Waliyullahi Akorede Husain, Elohor Precious Samuel, Wonder Olanipekun Oloruntoba, Fatmah Opeyemi Saka, Khalid Ayinde Oyelami, Mariam Temitope Baker

Al-Bahir

Antimicrobial resistance in Staphylococcus aureus is a serious global health problem as the organism rapidly develops resistance against widely used antibiotics. This study sought to investigate the antibacterial and antibiofilm properties of γ-Tocopherol, a natural compound from Ocimum gratissimum, as well as its synergism with 5-hydroxymethylfurfural (5-HMF) against S. aureus. The antibacterial activities and minimum inhibitory concentrations of the compounds were determined using agar diffusion and microbroth dilution methods, respectively. Biofilm reduction was evaluated using 2,3,5-triphenyltetrazolium chloride (TTC) assay and membrane integrity was evaluated using the crystal violet microtiter plate assay and the ion leakage assay. The results …

Hiv-1 Tat-Driven Glutamate Dysregulation: Implications For Cognitive Impairment In Hand, Brenna Duffy, Michael Nonnemacher, Sandhya Kortagere

Kimmel Cancer Center Faculty Papers

PURPOSE OF REVIEW: HIV-1-associated neurocognitive disorders (HAND) manifest in 15% to 50% of people with HIV, impairing learning and memory and executive function. The chronic generation of HIV-1 Transactivator of transcription (Tat) likely contributes to HAND via direct neuronal toxicity and glial-mediated toxicity. This review summarizes our current understanding of how chronic Tat generation from microglia and astrocytes promote glutamate excitotoxicity.

RECENT FINDINGS: In recent years, the indirect effects of Tat through the activation of glial cells have gained significant interest. This review highlights microglia and astrocytes as HIV-1 reservoirs that release Tat protein in the central nervous system. Specific …

Impact Of Dolutegravir-Based Regimens On Patient Satisfaction And Quality Of Life Among People Living With Hiv: A Systematic Review And Meta-Analysis, Mustapha Muhammed Abubakar, Christabel Ogechukwu Okoye, Ruth Jeminiwa, Ifeanyi Kanayo Ifeorah, Lotanna Ezeja, Yusuf Dauran, Sahabi Musa, Silas Usen Joel, Abdurrahman Murtala Bello, Amauche Pearl Ngige, Gabriel Ezenri, Abdulmuminu Isah, Ifunanya Ikhile, Blessing Onyinye Ukoha-Kalu

College of Pharmacy Faculty Papers

Background: Despite the global scale up of dolutegravir (DTG)-based regimens as the preferred first-line therapy for persons living with HIV (PLHIV), no comprehensive evidence exists on its effect on patient-reported outcomes such as Quality of Life (QoL) and patient satisfaction (PS). We conducted a systematic review and meta-analysis to provide the first comprehensive quantitative synthesis of the effect of DTG-based regimens on QoL and PS among PLHIV.

Method: We conducted literature search on PubMed, Scopus, Embase and Cochrane Library databases for peer-reviewed, primary studies published from January 2015 to January 2025. Studies using validated tools to evaluate QoL and PS …